The hardness of approximation: gap location
Computational Complexity
A Linear-Time Algorithm for Finding Tree-Decompositions of Small Treewidth
SIAM Journal on Computing
Haplotyping as perfect phylogeny: conceptual framework and efficient solutions
Proceedings of the sixth annual international conference on Computational biology
Computers and Intractability: A Guide to the Theory of NP-Completeness
Computers and Intractability: A Guide to the Theory of NP-Completeness
A Practical Algorithm for Optimal Inference of Haplotypes from Diploid Populations
Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology
A note on the single genotype resolution problem
Journal of Computer Science and Technology
An approximation algorithm for haplotype inference by maximum parsimony
Proceedings of the 2005 ACM symposium on Applied computing
Islands of Tractability for Parsimony Haplotyping
CSB '05 Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference
Haplotyping Populations by Pure Parsimony: Complexity of Exact and Approximation Algorithms
INFORMS Journal on Computing
Haplotype inference by pure Parsimony
CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Computational Complexity of Perfect-Phylogeny-Related Haplotyping Problems
MFCS '08 Proceedings of the 33rd international symposium on Mathematical Foundations of Computer Science
A Set-Covering Approach with Column Generation for Parsimony Haplotyping
INFORMS Journal on Computing
Haplotype Inference Constrained by Plausible Haplotype Data
CPM '09 Proceedings of the 20th Annual Symposium on Combinatorial Pattern Matching
CollHaps: A Heuristic Approach to Haplotype Inference by Parsimony
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Phylogeny - and parsimony-based haplotype inference with constraints
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Extended islands of tractability for parsimony haplotyping
CPM'10 Proceedings of the 21st annual conference on Combinatorial pattern matching
Pure Parsimony Xor Haplotyping
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
Haplotype Inference Constrained by Plausible Haplotype Data
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
WABI'06 Proceedings of the 6th international conference on Algorithms in Bioinformatics
The clark phase-able sample size problem: long-range phasing and loss of heterozygosity in GWAS
RECOMB'10 Proceedings of the 14th Annual international conference on Research in Computational Molecular Biology
Phylogeny- and parsimony-based haplotype inference with constraints
Information and Computation
FNphasing: A Novel Fast Heuristic Algorithm for Haplotype Phasing Based on Flow Network Model
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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We study the parsimony approach to haplotype inference, which calls for finding a set of haplotypes of minimum cardinality that explains an input set of genotypes. We prove that the problem is APX-hard even in very restricted cases. On the positive side, we identify islands of tractability for the problem, by focusing on instances with specific structure of haplotype sharing among the input genotypes. We exploit the structure of those instance to give polynomial and constant-approximation algorithms to the problem. We also show that the general parsimony haplotyping problem is fixed parameter tractable.